1
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Shimshon A, Dahan K, Israel-Gueta M, Olmayev-Yaakobov D, Timms RT, Bekturova A, Makaros Y, Elledge SJ, Koren I. Dipeptidyl peptidases and E3 ligases of N-degron pathways cooperate to regulate protein stability. J Cell Biol 2024; 223:e202311035. [PMID: 38874443 PMCID: PMC11178506 DOI: 10.1083/jcb.202311035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 06/15/2024] Open
Abstract
N-degrons are short sequences located at protein N-terminus that mediate the interaction of E3 ligases (E3s) with substrates to promote their proteolysis. It is well established that N-degrons can be exposed following protease cleavage to allow recognition by E3s. However, our knowledge regarding how proteases and E3s cooperate in protein quality control mechanisms remains minimal. Using a systematic approach to monitor the protein stability of an N-terminome library, we found that proline residue at the third N-terminal position (hereafter "P+3") promotes instability. Genetic perturbations identified the dipeptidyl peptidases DPP8 and DPP9 and the primary E3s of N-degron pathways, UBR proteins, as regulators of P+3 bearing substrate turnover. Interestingly, P+3 UBR substrates are significantly enriched for secretory proteins. We found that secretory proteins relying on a signal peptide (SP) for their targeting contain a "built-in" N-degron within their SP. This degron becomes exposed by DPP8/9 upon translocation failure to the designated compartments, thus enabling clearance of mislocalized proteins by UBRs to maintain proteostasis.
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Affiliation(s)
- Adi Shimshon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Karin Dahan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Mor Israel-Gueta
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Diana Olmayev-Yaakobov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre , Cambridge, UK
| | - Aizat Bekturova
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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2
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Chang YT, Barad BA, Rahmani H, Zid BM, Grotjahn DA. Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.604013. [PMID: 39071314 PMCID: PMC11275913 DOI: 10.1101/2024.07.17.604013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Most of the mitochondria proteome is nuclear-encoded, synthesized by cytoplasmic ribosomes, and targeted to mitochondria post-translationally. However, a subset of mitochondrial-targeted proteins is imported co-translationally, although the molecular mechanisms governing this process remain unclear. We employ cellular cryo-electron tomography to visualize interactions between cytoplasmic ribosomes and mitochondria in Saccharomyces cerevisiae . We use surface morphometrics tools to identify a subset of ribosomes optimally oriented on mitochondrial membranes for protein import. This allows us to establish the first subtomogram average structure of a cytoplasmic ribosome on the surface of the mitochondria in the native cellular context, which showed three distinct connections with the outer mitochondrial membrane surrounding the peptide exit tunnel. Further, this analysis demonstrated that cytoplasmic ribosomes primed for mitochondrial protein import cluster on the outer mitochondrial membrane at sites of local constrictions of the outer and inner mitochondrial membrane. Overall, our study reveals the architecture and the spatial organization of cytoplasmic ribosomes at the mitochondrial surface, providing a native cellular context to define the mechanisms that mediate efficient mitochondrial co-translational protein import. SUMMARY Chang et al. present a membrane-guided approach for identifying a subset of cytoplasmic ribosomes oriented for protein import on the mitochondrial surface in Saccharomyces cerevisiae using cryo-electron tomography. They show that ribosomes cluster, make multiple contacts with, and induce local changes to the mitochondrial membrane ultrastructure at import sites.
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3
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Liu L, Wang H, Liu L, Cheng F, Aisa HA, Li C, Meng S. Rupestonic Acid Derivative YZH-106 Promotes Lysosomal Degradation of HBV L- and M-HBsAg via Direct Interaction with PreS2 Domain. Viruses 2024; 16:1151. [PMID: 39066313 PMCID: PMC11281537 DOI: 10.3390/v16071151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/13/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Hepatitis B surface antigen (HBsAg) is not only the biomarker of hepatitis B virus (HBV) infection and expression activity in hepatocytes, but it also contributes to viral specific T cell exhaustion and HBV persistent infection. Therefore, anti-HBV therapies targeting HBsAg to achieve HBsAg loss are key approaches for an HBV functional cure. In this study, we found that YZH-106, a rupestonic acid derivative, inhibited HBsAg secretion and viral replication. Further investigation demonstrated that YZH-106 promoted the lysosomal degradation of viral L- and M-HBs proteins. A mechanistic study using Biacore and docking analysis revealed that YZH-106 bound directly to the PreS2 domain of L- and M-HBsAg, thereby blocking their entry into the endoplasmic reticulum (ER) and promoting their degradation in cytoplasm. Our work thereby provides the basis for the design of a novel compound therapy to target HBsAg against HBV infection.
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Affiliation(s)
- Lanlan Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Haoyu Wang
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lulu Liu
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Fang Cheng
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Haji Akber Aisa
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Changfei Li
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
| | - Songdong Meng
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.L.); (H.W.); (L.L.)
- University of Chinese Academy of Sciences, Beijing 100101, China
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4
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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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5
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Robeson L, Casanova‐Morales N, Burgos‐Bravo F, Alfaro‐Valdés HM, Lesch R, Ramírez‐Álvarez C, Valdivia‐Delgado M, Vega M, Matute RA, Schekman R, Wilson CAM. Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers. Protein Sci 2024; 33:e4996. [PMID: 38747383 PMCID: PMC11094780 DOI: 10.1002/pro.4996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
The Sec61 translocon allows the translocation of secretory preproteins from the cytosol to the endoplasmic reticulum lumen during polypeptide biosynthesis. These proteins possess an N-terminal signal peptide (SP) which docks at the translocon. SP mutations can abolish translocation and cause diseases, suggesting an essential role for this SP/Sec61 interaction. However, a detailed biophysical characterization of this binding is still missing. Here, optical tweezers force spectroscopy was used to characterize the kinetic parameters of the dissociation process between Sec61 and the SP of prepro-alpha-factor. The unbinding parameters including off-rate constant and distance to the transition state were obtained by fitting rupture force data to Dudko-Hummer-Szabo models. Interestingly, the translocation inhibitor mycolactone increases the off-rate and accelerates the SP/Sec61 dissociation, while also weakening the interaction. Whereas the translocation deficient mutant containing a single point mutation in the SP abolished the specificity of the SP/Sec61 binding, resulting in an unstable interaction. In conclusion, we characterize quantitatively the dissociation process between the signal peptide and the translocon, and how the unbinding parameters are modified by a translocation inhibitor.
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Affiliation(s)
- Luka Robeson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Nathalie Casanova‐Morales
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- Facultad de Artes LiberalesUniversidad Adolfo IbáñezSantiagoChile
| | - Francesca Burgos‐Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- California Institute for Quantitative Biosciences, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Hilda M. Alfaro‐Valdés
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Robert Lesch
- Department of Molecular and Cellular Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Carolina Ramírez‐Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Mauricio Valdivia‐Delgado
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Ricardo A. Matute
- Centro Integrativo de Biología y Química Aplicada (CIBQA)Universidad Bernardo O'HigginsSantiagoChile
- Division of Chemistry and Chemical EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Randy Schekman
- Department of Molecular and Cellular Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
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6
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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7
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Shin MK, Chang J, Park J, Lee HJ, Woo JS, Kim YK. Nonsense-mediated mRNA decay of mRNAs encoding a signal peptide occurs primarily after mRNA targeting to the endoplasmic reticulum. Mol Cells 2024; 47:100049. [PMID: 38513766 PMCID: PMC11016901 DOI: 10.1016/j.mocell.2024.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024] Open
Abstract
Translation of messenger ribonucleic acids (mRNAs) encoding integral membrane proteins or secreted proteins occurs on the surface of the endoplasmic reticulum (ER). When a nascent signal peptide is synthesized from the mRNAs, the ribosome-nascent chain complex (RNC) is recognized by the signal recognition particle (SRP) and then transported to the surface of the ER. The appropriate targeting of the RNC-SRP complex to the ER is monitored by a quality control pathway, a nuclear cap-binding complex (CBC)-ensured translational repression of RNC-SRP (CENTRE). In this study, using ribosome profiling of CBC-associated and eukaryotic translation initiation factor 4E-associated mRNAs, we reveal that, at the transcriptomic level, CENTRE is in charge of the translational repression of the CBC-RNC-SRP until the complex is specifically transported to the ER. We also find that CENTRE inhibits the nonsense-mediated mRNA decay (NMD) of mRNAs within the CBC-RNC-SRP. The NMD occurs only after the CBC-RNC-SRP is targeted to the ER and after eukaryotic translation initiation factor 4E replaces CBC. Our data indicate dual surveillance for properly targeting mRNAs encoding integral membrane or secretory proteins to the ER. CENTRE blocks gene expression at the translation level before the CBC-RNC-SRP delivery to the ER, and NMD monitors mRNA quality after its delivery to the ER.
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Affiliation(s)
- Min-Kyung Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joori Park
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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8
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Cohen B, Golani-Armon A, Arava YS. Emerging implications for ribosomes in proximity to mitochondria. Semin Cell Dev Biol 2024; 154:123-130. [PMID: 36642616 DOI: 10.1016/j.semcdb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/11/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023]
Abstract
Synthesis of all proteins in eukaryotic cells, apart from a few organellar proteins, is done by cytosolic ribosomes. Many of these ribosomes are localized in the vicinity of the functional site of their encoded protein, enabling local protein synthesis. Studies in various organisms and tissues revealed that such locally translating ribosomes are also present near mitochondria. Here, we provide a brief summary of evidence for localized translation near mitochondria, then present data suggesting that these localized ribosomes may enable local translational regulatory processes in response to mitochondria needs. Finally, we describe the involvement of such localized ribosomes in the quality control of protein synthesis and mitochondria. These emerging views suggest that ribosomes localized near mitochondria are a hub for a variety of activities with diverse implications on mitochondria physiology.
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Affiliation(s)
- Bar Cohen
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Adi Golani-Armon
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Yoav S Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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9
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Bittner E, Stehlik T, Lam J, Dimitrov L, Heimerl T, Schöck I, Harberding J, Dornes A, Heymons N, Bange G, Schuldiner M, Zalckvar E, Bölker M, Schekman R, Freitag J. Proteins that carry dual targeting signals can act as tethers between peroxisomes and partner organelles. PLoS Biol 2024; 22:e3002508. [PMID: 38377076 PMCID: PMC10906886 DOI: 10.1371/journal.pbio.3002508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/01/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Peroxisomes are organelles with crucial functions in oxidative metabolism. To correctly target to peroxisomes, proteins require specialized targeting signals. A mystery in the field is the sorting of proteins that carry a targeting signal for peroxisomes and as well as for other organelles, such as mitochondria or the endoplasmic reticulum (ER). Exploring several of these proteins in fungal model systems, we observed that they can act as tethers bridging organelles together to create contact sites. We show that in Saccharomyces cerevisiae this mode of tethering involves the peroxisome import machinery, the ER-mitochondria encounter structure (ERMES) at mitochondria and the guided entry of tail-anchored proteins (GET) pathway at the ER. Our findings introduce a previously unexplored concept of how dual affinity proteins can regulate organelle attachment and communication.
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Affiliation(s)
- Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jason Lam
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Lazar Dimitrov
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Thomas Heimerl
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Isabelle Schöck
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Jannik Harberding
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Nikola Heymons
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Randy Schekman
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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10
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Schlößer M, Ugalde JM, Meyer AJ. Visualizing Orientation and Topology of ER Membrane Proteins In Planta. Methods Mol Biol 2024; 2772:371-382. [PMID: 38411829 DOI: 10.1007/978-1-0716-3710-4_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The orientation of membrane proteins within the lipid bilayer is key to understanding their molecular function. Similarly, the proper topology of multispanning membrane proteins is crucial for their function. Although bioinformatics tools can predict these parameters assessing the presence of hydrophobic protein domains sufficiently long to span the membrane and other structural features, the predictions from different algorithms are often inconsistent. Therefore, experimental analysis becomes mandatory. Redox-based topology analysis exploits the steep gradient in the glutathione redox potential (EGSH) across the ER membrane of about 80 mV to visualize the orientation of ER membrane proteins by fusing the EGSH biosensor roGFP2 to either the N- or the C-termini of the investigated protein sequence. Transient expression of these fusion proteins in tobacco leaves allows direct visualization of orientation and topology of ER membrane proteins in planta. The protocol outlined here is based on either a simple merge of the two excitation channels of roGFP2 or a colocalization analysis of the two channels and thus avoids ratiometric analysis of roGFP2 fluorescence.
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Affiliation(s)
| | - José M Ugalde
- INRES-Chemical Signalling, University of Bonn, Bonn, Germany
| | - Andreas J Meyer
- INRES-Chemical Signalling, University of Bonn, Bonn, Germany.
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11
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Piña F, Yan B, Hu J, Niwa M. Reticulons bind sphingolipids to activate the endoplasmic reticulum cell cycle checkpoint, the ER surveillance pathway. Cell Rep 2023; 42:113403. [PMID: 37979174 DOI: 10.1016/j.celrep.2023.113403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2022] [Accepted: 10/23/2023] [Indexed: 11/20/2023] Open
Abstract
The inheritance of a functional endoplasmic reticulum (ER) is ensured by the ER stress surveillance (ERSU) pathway. Here, we made the unexpected discovery that reticulon 1 (Rtn1) and Yop1, well-known ER-curvature-generating proteins, each possess two sphingolipid-binding motifs within their transmembrane domains and that these motifs recognize the ER-stress-induced sphingolipid phytosphingosine (PHS), resulting in an ER inheritance block. Upon binding PHS, Rtn1/Yop1 accumulate on the ER tubule, poised to enter the emerging daughter cell, and cause its misdirection to the bud scars (i.e., previous cell division sites). Amino acid changes in the conserved PHS-binding motifs preclude Rtn1 or Yop1 from binding PHS and diminish their enrichment on the tubular ER, ultimately preventing the ER-stress-induced inheritance block. Conservation of these sphingolipid-binding motifs in human reticulons suggests that sphingolipid binding to Rtn1 and Yop1 represents an evolutionarily conserved mechanism that enables cells to respond to ER stress.
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Affiliation(s)
- Francisco Piña
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA
| | - Bing Yan
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Junjie Hu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Rm. 6210, Chaoyang District, Beijing 100101, China
| | - Maho Niwa
- Division of Biological Sciences, Molecular Biology Section, University of California, San Diego, NSB#1, Rm. 5328, 9500 Gilman Drive, San Diego, CA 92093-0377, USA.
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12
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Gutierrez Guarnizo SA, Kellogg MK, Miller SC, Tikhonova E, Karamysheva ZN, Karamyshev AL. Pathogenic signal peptide variants in the human genome. NAR Genom Bioinform 2023; 5:lqad093. [PMID: 37859801 PMCID: PMC10583284 DOI: 10.1093/nargab/lqad093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/05/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Secreted and membrane proteins represent a third of all cellular proteins and contain N-terminal signal peptides that are required for protein targeting to endoplasmic reticulum (ER). Mutations in signal peptides affect protein targeting, translocation, processing, and stability, and are associated with human diseases. However, only a few of them have been identified or characterized. In this report, we identified pathogenic signal peptide variants across the human genome using bioinformatic analyses and predicted the molecular mechanisms of their pathology. We recovered more than 65 thousand signal peptide mutations, over 11 thousand we classified as pathogenic, and proposed framework for distinction of their molecular mechanisms. The pathogenic mutations affect over 3.3 thousand genes coding for secreted and membrane proteins. Most pathogenic mutations alter the signal peptide hydrophobic core, a critical recognition region for the signal recognition particle, potentially activating the Regulation of Aberrant Protein Production (RAPP) quality control and specific mRNA degradation. The remaining pathogenic variants (about 25%) alter either the N-terminal region or signal peptidase processing site that can result in translocation deficiencies at the ER membrane or inhibit protein processing. This work provides a conceptual framework for the identification of mutations across the genome and their connection with human disease.
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Affiliation(s)
| | - Morgana K Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Sarah C Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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13
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Zhou Q, Yang Y, Xu Z, Deng K, Zhang Z, Hao J, Li N, Wang Y, Wang Z, Chen H, Yang Y, Xiao F, Zhang X, Gao S, Li Y. ATAD1 inhibits hepatitis C virus infection by removing the viral TA-protein NS5B from mitochondria. EMBO Rep 2023; 24:e56614. [PMID: 37789674 PMCID: PMC10626439 DOI: 10.15252/embr.202256614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
ATPase family AAA domain-containing protein 1 (ATAD1) maintains mitochondrial homeostasis by removing mislocalized tail-anchored (TA) proteins from the mitochondrial outer membrane (MOM). Hepatitis C virus (HCV) infection induces mitochondrial fragmentation, and viral NS5B protein is a TA protein. Here, we investigate whether ATAD1 plays a role in regulating HCV infection. We find that HCV infection has no effect on ATAD1 expression, but knockout of ATAD1 significantly enhances HCV infection; this enhancement is suppressed by ATAD1 complementation. NS5B partially localizes to mitochondria, dependent on its transmembrane domain (TMD), and induces mitochondrial fragmentation, which is further enhanced by ATAD1 knockout. ATAD1 interacts with NS5B, dependent on its three internal domains (TMD, pore-loop 1, and pore-loop 2), and induces the proteasomal degradation of NS5B. In addition, we provide evidence that ATAD1 augments the antiviral function of MAVS upon HCV infection. Taken together, we show that the mitochondrial quality control exerted by ATAD1 can be extended to a novel antiviral function through the extraction of the viral TA-protein NS5B from the mitochondrial outer membrane.
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Affiliation(s)
- Qing Zhou
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Technology Center, China Tobacco Henan Industrial Co., LtdZhengzhouChina
- Department of Infectious DiseasesThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Yuhao Yang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Zhanxue Xu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Kai Deng
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Guangzhou Eighth People's HospitalGuangzhou Medical UniversityGuangzhouChina
| | - Zhenzhen Zhang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Jiawei Hao
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ni Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Department of Infectious DiseasesThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Yanling Wang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Haihang Chen
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Yang Yang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Fei Xiao
- Department of Infectious DiseaseThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
| | - Xiaohong Zhang
- Department of Infectious DiseasesThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouChina
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yi‐Ping Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, and Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Department of Infectious DiseasesThe Third Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouChina
- Department of Infectious DiseaseThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiChina
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14
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Jung M, Zimmermann R. Quantitative Mass Spectrometry Characterizes Client Spectra of Components for Targeting of Membrane Proteins to and Their Insertion into the Membrane of the Human ER. Int J Mol Sci 2023; 24:14166. [PMID: 37762469 PMCID: PMC10532041 DOI: 10.3390/ijms241814166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
To elucidate the redundancy in the components for the targeting of membrane proteins to the endoplasmic reticulum (ER) and/or their insertion into the ER membrane under physiological conditions, we previously analyzed different human cells by label-free quantitative mass spectrometry. The HeLa and HEK293 cells had been depleted of a certain component by siRNA or CRISPR/Cas9 treatment or were deficient patient fibroblasts and compared to the respective control cells by differential protein abundance analysis. In addition to clients of the SRP and Sec61 complex, we identified membrane protein clients of components of the TRC/GET, SND, and PEX3 pathways for ER targeting, and Sec62, Sec63, TRAM1, and TRAP as putative auxiliary components of the Sec61 complex. Here, a comprehensive evaluation of these previously described differential protein abundance analyses, as well as similar analyses on the Sec61-co-operating EMC and the characteristics of the topogenic sequences of the various membrane protein clients, i.e., the client spectra of the components, are reported. As expected, the analysis characterized membrane protein precursors with cleavable amino-terminal signal peptides or amino-terminal transmembrane helices as predominant clients of SRP, as well as the Sec61 complex, while precursors with more central or even carboxy-terminal ones were found to dominate the client spectra of the SND and TRC/GET pathways for membrane targeting. For membrane protein insertion, the auxiliary Sec61 channel components indeed share the client spectra of the Sec61 complex to a large extent. However, we also detected some unexpected differences, particularly related to EMC, TRAP, and TRAM1. The possible mechanistic implications for membrane protein biogenesis at the human ER are discussed and can be expected to eventually advance our understanding of the mechanisms that are involved in the so-called Sec61-channelopathies, resulting from deficient ER protein import.
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Affiliation(s)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
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15
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Tipper DJ, Harley CA. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell. Front Cell Dev Biol 2023; 11:1220441. [PMID: 37635876 PMCID: PMC10456885 DOI: 10.3389/fcell.2023.1220441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
DNA replication, transcription, and translation in eukaryotic cells occur with decreasing but still high fidelity. In contrast, for the estimated 33% of the human proteome that is inserted as transmembrane (TM) proteins, insertion with a non-functional inverted topology is frequent. Correct topology is essential for function and trafficking to appropriate cellular compartments and is controlled principally by responses to charged residues within 15 residues of the inserted TM domain (TMD); the flank with the higher positive charge remains in the cytosol (inside), following the positive inside rule (PIR). Yeast (Saccharomyces cerevisiae) mutants that increase insertion contrary to the PIR were selected. Mutants with strong phenotypes were found only in SPF1 and STE24 (human cell orthologs are ATP13A1 and ZMPSte24) with, at the time, no known relevant functions. Spf1/Atp13A1 is now known to dislocate to the cytosol TM proteins inserted contrary to the PIR, allowing energy-conserving reinsertion. We hypothesize that Spf1 and Ste24 both recognize the short, positively charged ER luminal peptides of TM proteins inserted contrary to the PIR, accepting these peptides into their large membrane-spanning, water-filled cavities through interaction with their many interior surface negative charges. While entry was demonstrated for Spf1, no published evidence directly demonstrates substrate entry to the Ste24 cavity, internal access to its zinc metalloprotease (ZMP) site, or active withdrawal of fragments, which may be essential for function. Spf1 and Ste24 comprise a PIR quality control system that is conserved in all eukaryotes and presumably evolved in prokaryotic progenitors as they gained differentiated membrane functions. About 75% of the PIR is imposed by this quality control system, which joins the UPR, ERAD, and autophagy (ER-phagy) in coordinated, overlapping quality control of ER protein function.
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Affiliation(s)
- Donald J. Tipper
- University of Massachusetts Medical School, Worcester, MA, United States
| | - Carol A. Harley
- i3S-Instituto de Investigação e Inovação em Saude, Universidade do Porto, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
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16
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Sarmento MJ, Llorente A, Petan T, Khnykin D, Popa I, Nikolac Perkovic M, Konjevod M, Jaganjac M. The expanding organelle lipidomes: current knowledge and challenges. Cell Mol Life Sci 2023; 80:237. [PMID: 37530856 PMCID: PMC10397142 DOI: 10.1007/s00018-023-04889-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lipids in cell membranes and subcellular compartments play essential roles in numerous cellular processes, such as energy production, cell signaling and inflammation. A specific organelle lipidome is characterized by lipid synthesis and metabolism, intracellular trafficking, and lipid homeostasis in the organelle. Over the years, considerable effort has been directed to the identification of the lipid fingerprints of cellular organelles. However, these fingerprints are not fully characterized due to the large variety and structural complexity of lipids and the great variability in the abundance of different lipid species. The process becomes even more challenging when considering that the lipidome differs in health and disease contexts. This review summarizes the information available on the lipid composition of mammalian cell organelles, particularly the lipidome of the nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus, plasma membrane and organelles in the endocytic pathway. The lipid compositions of extracellular vesicles and lamellar bodies are also described. In addition, several examples of subcellular lipidome dynamics under physiological and pathological conditions are presented. Finally, challenges in mapping organelle lipidomes are discussed.
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Affiliation(s)
- Maria J Sarmento
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379, Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167, Oslo, Norway
- Faculty of Medicine, Centre for Cancer Cell Reprogramming, University of Oslo, Montebello, 0379, Oslo, Norway
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Denis Khnykin
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Iuliana Popa
- Pharmacy Department, Bâtiment Henri Moissan, University Paris-Saclay, 17 Avenue des Sciences, 91400, Orsay, France
| | | | - Marcela Konjevod
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia
| | - Morana Jaganjac
- Division of Molecular Medicine, Ruder Boskovic Institute, 10000, Zagreb, Croatia.
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17
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Legesse A, Kaushansky N, Braunstein I, Saad H, Lederkremer G, Navon A, Stanhill A. The role of RNF149 in the pre-emptive quality control substrate ubiquitination. Commun Biol 2023; 6:385. [PMID: 37031316 PMCID: PMC10082771 DOI: 10.1038/s42003-023-04763-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/27/2023] [Indexed: 04/10/2023] Open
Abstract
Protein quality control is a process in which a protein's folding status is constantly monitored. Mislocalized proteins (MLP), are processed by the various quality control pathways, as they are often misfolded due to inappropriate cellular surroundings. Polypeptides that fail to translocate into the ER due to an inefficient signal peptide, mutations or ER stress are recognized by the pre-emptive ER associated quality control (pEQC) pathway and degraded by the 26 S proteasome. In this report we reveal the role of RNF149, a membrane bound E3 ligase in the ubiquitination of known pEQC substrates. We demonstrate its selective binding only to non-translocated proteins and its association with known pEQC components. Impairment in RNF149 function increases translocation flux into the ER and manifests in a myeloproliferative neoplasm (MPN) phenotype, a pathological condition associated with pEQC impairment. Finally, the dynamic localization of RNF149 may provide a molecular switch to regulate pEQC during ER stress.
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Affiliation(s)
- Aster Legesse
- Department of Natural and Life Sciences, Open University of Israel, Ra'anana, 43710, Israel
| | - Nathali Kaushansky
- Department of Molecular Cell Biology, Weizmann institute of Science, Rehovot, 7610001, Israel
| | - Ilana Braunstein
- Department of Biochemistry, Technion School of Medicine, Haifa, 31096, Israel
| | - Haddas Saad
- The Shmunis School of Biomedicine and Cancer Research, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Gerardo Lederkremer
- The Shmunis School of Biomedicine and Cancer Research, George Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Ami Navon
- Department of Immunology and Regenerative Biology, Weizmann institute of Science, Rehovot, 7610001, Israel
| | - Ariel Stanhill
- Department of Natural and Life Sciences, Open University of Israel, Ra'anana, 43710, Israel.
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18
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Jansen RL, van den Noort M, Krikken AM, Bibi C, Böhm A, Schuldiner M, Zalckvar E, van der Klei IJ. Novel targeting assay uncovers targeting information within peroxisomal ABC transporter Pxa1. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2023; 1870:119471. [PMID: 37028652 DOI: 10.1016/j.bbamcr.2023.119471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023]
Abstract
The mechanism behind peroxisomal membrane protein targeting is still poorly understood, with only two yeast proteins believed to be involved and no consensus targeting sequence. Pex19 is thought to bind peroxisomal membrane proteins in the cytosol, and is subsequently recruited by Pex3 at the peroxisomal surface, followed by protein insertion via a mechanism that is as-yet-unknown. However, some peroxisomal membrane proteins still correctly sort in the absence of Pex3 or Pex19, suggesting that multiple sorting pathways exist. Here, we studied sorting of yeast peroxisomal ABC transporter Pxa1. Co-localization analysis of Pxa1-GFP in a collection of 86 peroxisome-related deletion strains revealed that Pxa1 sorting requires Pex3 and Pex19, while none of the other 84 proteins tested were essential. To identify regions with peroxisomal targeting information in Pxa1, we developed a novel in vivo re-targeting assay, using a reporter consisting of the mitochondrial ABC transporter Mdl1 lacking its N-terminal mitochondrial targeting signal. Using this assay, we showed that the N-terminal 95 residues of Pxa1 are sufficient for retargeting this reporter to peroxisomes. Interestingly, truncated Pxa1 lacking residues 1-95 still localized to peroxisomes. This was confirmed via localization of various Pxa1 truncation and deletion constructs. However, localisation of Pxa1 lacking residues 1-95 depended on the presence of its interaction partner Pxa2, indicating that this truncated protein does not contain a true targeting signal.
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19
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Xu S, Li X, Geng J, Cao Y, Yu Y, Qi L. Sec61γ is a vital protein in the endoplasmic reticulum membrane promoting tumor metastasis and invasion in lung adenocarcinoma. Br J Cancer 2023; 128:1478-1490. [PMID: 36759724 PMCID: PMC10070493 DOI: 10.1038/s41416-023-02150-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/01/2022] [Accepted: 01/11/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is one of the most common malignant tumors worldwide. Finding effective prognostic markers and therapeutic targets is of great significance for controlling metastasis and invasion clinically. METHODS The open copy-number aberrations and gene expression datasets were analysed, and the data of 102 LUAD patients was used for further validation. The cell proliferation, colony formation, migration, invasion assays and mice tumor models were used to detect the function of SEC61G. The epidermal growth factor receptor (EGFR) pathway was also detected to find the mechanism of Sec61γ. RESULTS Based on the open datasets, we found that the high level of SEC61G mRNA may drive LUAD metastasis. Furthermore, the overexpression of Sec61γ protein was significantly associated with poor prognosis and greater tumor cell proliferation and metastasis. The SEC61G knockdown could inhibit the EGFR pathway, including STAT3, AKT and PI3K, which can be reversed by Sec61γ overexpression and epithelial growth factor (EGF) supplement. CONCLUSIONS Sec61γ promoted the proliferation, metastasis, and invasion of LUAD through EGFR pathways. Sec61γ might be a potential target for the treatment of LUAD metastases.
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Affiliation(s)
- Shanqi Xu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianxiong Geng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yingyue Cao
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yan Yu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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20
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Yifrach E, Rudowitz M, Cruz-Zaragoza LD, Tirosh A, Gazi Z, Peleg Y, Kunze M, Eisenstein M, Schliebs W, Schuldiner M, Erdmann R, Zalckvar E. Determining the targeting specificity of the selective peroxisomal targeting factor Pex9. Biol Chem 2023; 404:121-133. [PMID: 36279206 DOI: 10.1515/hsz-2022-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
Abstract
Accurate and regulated protein targeting is crucial for cellular function and proteostasis. In the yeast Saccharomyces cerevisiae, peroxisomal matrix proteins, which harboring a Peroxisomal Targeting Signal 1 (PTS1), can utilize two paralog targeting factors, Pex5 and Pex9, to target correctly. While both proteins are similar and recognize PTS1 signals, Pex9 targets only a subset of Pex5 cargo proteins. However, what defines this substrate selectivity remains uncovered. Here, we used unbiased screens alongside directed experiments to identify the properties underlying Pex9 targeting specificity. We find that the specificity of Pex9 is largely determined by the hydrophobic nature of the amino acid preceding the PTS1 tripeptide of its cargos. This is explained by structural modeling of the PTS1-binding cavities of the two factors showing differences in their surface hydrophobicity. Our work outlines the mechanism by which targeting specificity is achieved, enabling dynamic rewiring of the peroxisomal proteome in changing metabolic needs.
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Affiliation(s)
- Eden Yifrach
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Luis Daniel Cruz-Zaragoza
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Asa Tirosh
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Gazi
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain research, Medical University of Vienna, Spitalgasse 4, A-1090 Vienna, Austria
| | - Miriam Eisenstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
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21
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Tang X, Pu Y, Peng H, Li K, Faouzi S, Lu T, Pu D, Cerezo M, Xu J, Li L, Robert C, Shen S. Spatial patterns of the cap-binding complex eIF4F in human melanoma cells. Comput Struct Biotechnol J 2023; 21:1157-1168. [PMID: 36789267 PMCID: PMC9918392 DOI: 10.1016/j.csbj.2023.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/01/2023] Open
Abstract
As a central node of protein synthesis, the cap-binding complex, eukaryotic translation initiation factor 4 F (eIF4F), is involved in cell homeostasis, development and tumorigenesis. A large body of literature exists on the regulation and function of eIF4F in cancer cells, however the intracellular localization patterns of this complex are largely unknown. Since different subsets of mRNAs are translated in distinct subcellular compartments, understanding the distribution of translation initiation factors in the cell is of major interest. Here, we developed an in situ detection method for eIF4F at the single cell level. By using an image-based spot feature analysis pipeline as well as supervised machine learning, we identify five distinct spatial patterns of the eIF4F translation initiation complex in human melanoma cells. The quantity of eIF4F complex per cell correlated with the global mRNA translation activity, and its variation is dynamically regulated by cell state or extracellular stimuli. In contrast, the spatial patterns of eIF4F complexes at the single cell level could distinguish melanoma cells harboring different oncogenic driver mutations. This suggests that different tumorigenic contexts differentially regulate the subcellular localization of mRNA translation, with specific localization of eIF4F potentially associated with melanoma cell chemoresistance.
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Affiliation(s)
- Xinpu Tang
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu, China
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Pu
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
- Department of Burn Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Haoning Peng
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Kaixiu Li
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
| | - Sara Faouzi
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
| | - Tianjian Lu
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Dan Pu
- Lung Cancer Center, West China Hospital of Sichuan University, Chengdu, China
| | - Michael Cerezo
- Université Côte d′Azur, Nice, France
- Centre Méditerranéen de Médicine Moléculaire (C3M), INSERM U1065, Equipe 12, Nice, France
| | - Jianguo Xu
- Department of Neurosurgery, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Li
- Lung Cancer Center, West China Hospital of Sichuan University, Chengdu, China
- Corresponding author.
| | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France
- Dermatology Unit, Gustave Roussy Cancer Campus, Villejuif, France
- Corresponding author at: INSERM U981, Gustave Roussy Cancer Campus, Villejuif, France.
| | - Shensi Shen
- Institute of Thoracic Oncology, West China Hospital of Sichuan University, Chengdu, China
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
- Correspondence to: Institute of Thoracic Oncology and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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22
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Melnyk A, Lang S, Sicking M, Zimmermann R, Jung M. Co-chaperones of the Human Endoplasmic Reticulum: An Update. Subcell Biochem 2023; 101:247-291. [PMID: 36520310 DOI: 10.1007/978-3-031-14740-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In mammalian cells, the rough endoplasmic reticulum (ER) plays central roles in the biogenesis of extracellular plus organellar proteins and in various signal transduction pathways. For these reasons, the ER comprises molecular chaperones, which are involved in import, folding, assembly, export, plus degradation of polypeptides, and signal transduction components, such as calcium channels, calcium pumps, and UPR transducers plus adenine nucleotide carriers/exchangers in the ER membrane. The calcium- and ATP-dependent ER lumenal Hsp70, termed immunoglobulin heavy-chain-binding protein or BiP, is the central player in all these activities and involves up to nine different Hsp40-type co-chaperones, i.e., ER membrane integrated as well as ER lumenal J-domain proteins, termed ERj or ERdj proteins, two nucleotide exchange factors or NEFs (Grp170 and Sil1), and NEF-antagonists, such as MANF. Here we summarize the current knowledge on the ER-resident BiP/ERj chaperone network and focus on the interaction of BiP with the polypeptide-conducting and calcium-permeable Sec61 channel of the ER membrane as an example for BiP action and how its functional cycle is linked to ER protein import and various calcium-dependent signal transduction pathways.
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Affiliation(s)
- Armin Melnyk
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Mark Sicking
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany.
| | - Martin Jung
- Medical Biochemistry & Molecular Biology, Saarland University, Homburg, Germany
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23
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Sagarika P, Yadav K, Sahi C. Volleying plasma membrane proteins from birth to death: Role of J-domain proteins. Front Mol Biosci 2022; 9:1072242. [PMID: 36589230 PMCID: PMC9798423 DOI: 10.3389/fmolb.2022.1072242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
The function, stability, and turnover of plasma membrane (PM) proteins are crucial for cellular homeostasis. Compared to soluble proteins, quality control of plasma membrane proteins is extremely challenging. Failure to meet the high quality control standards is detrimental to cellular and organismal health. J-domain proteins (JDPs) are among the most diverse group of chaperones that collaborate with other chaperones and protein degradation machinery to oversee cellular protein quality control (PQC). Although fragmented, the available literature from different models, including yeast, mammals, and plants, suggests that JDPs assist PM proteins with their synthesis, folding, and trafficking to their destination as well as their degradation, either through endocytic or proteasomal degradation pathways. Moreover, some JDPs interact directly with the membrane to regulate the stability and/or functionality of proteins at the PM. The deconvoluted picture emerging is that PM proteins are relayed from one JDP to another throughout their life cycle, further underscoring the versatility of the Hsp70:JDP machinery in the cell.
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Lipid composition dependent binding of apolipoprotein E signal peptide: Importance of membrane cholesterol in protein trafficking. Biophys Chem 2022; 291:106907. [DOI: 10.1016/j.bpc.2022.106907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022]
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25
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O'Keefe S, Pool MR, High S. Membrane protein biogenesis at the ER: the highways and byways. FEBS J 2022; 289:6835-6862. [PMID: 33960686 DOI: 10.1111/febs.15905] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023]
Abstract
The Sec61 complex is the major protein translocation channel of the endoplasmic reticulum (ER), where it plays a central role in the biogenesis of membrane and secretory proteins. Whilst Sec61-mediated protein translocation is typically coupled to polypeptide synthesis, suggestive of significant complexity, an obvious characteristic of this core translocation machinery is its surprising simplicity. Over thirty years after its initial discovery, we now understand that the Sec61 complex is in fact the central piece of an elaborate jigsaw puzzle, which can be partly solved using new research findings. We propose that the Sec61 complex acts as a dynamic hub for co-translational protein translocation at the ER, proactively recruiting a range of accessory complexes that enhance and regulate its function in response to different protein clients. It is now clear that the Sec61 complex does not have a monopoly on co-translational insertion, with some transmembrane proteins preferentially utilising the ER membrane complex instead. We also have a better understanding of post-insertion events, where at least one membrane-embedded chaperone complex can capture the newly inserted transmembrane domains of multi-span proteins and co-ordinate their assembly into a native structure. Having discovered this array of Sec61-associated components and competitors, our next challenge is to understand how they act together in order to expand the range and complexity of the membrane proteins that can be synthesised at the ER. Furthermore, this diversity of components and pathways may open up new opportunities for targeted therapeutic interventions designed to selectively modulate protein biogenesis at the ER.
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Affiliation(s)
- Sarah O'Keefe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Martin R Pool
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stephen High
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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RNF185 regulates proteostasis in Ebolavirus infection by crosstalk between the calnexin cycle, ERAD, and reticulophagy. Nat Commun 2022; 13:6007. [PMID: 36224200 PMCID: PMC9554868 DOI: 10.1038/s41467-022-33805-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022] Open
Abstract
Virus infection affects cellular proteostasis and provides an opportunity to study this cellular process under perturbation. The proteostasis network in the endoplasmic reticulum (ER) is composed of the calnexin cycle, and the two protein degradation pathways ER-associated protein degradation (ERAD) and ER-to-lysosome-associated degradation (ERLAD/ER-phagy/reticulophagy). Here we show that calnexin and calreticulin trigger Zaire Ebolavirus (EBOV) glycoprotein GP1,2 misfolding. Misfolded EBOV-GP1,2 is targeted by ERAD machinery, but this results in lysosomal instead of proteasomal degradation. Moreover, the ER Ub ligase RNF185, usually associated with ERAD, polyubiquitinates EBOV-GP1,2 on lysine 673 via ubiquitin K27-linkage. Polyubiquinated GP1,2 is subsequently recruited into autophagosomes by the soluble autophagy receptor sequestosome 1 (SQSTM1/p62), in an ATG3- and ATG5-dependent manner. We conclude that EBOV hijacks all three proteostasis mechanisms in the ER to downregulate GP1,2 via polyubiquitination and show that this increases viral fitness. This study identifies linkages among proteostasis network components previously thought to function independently. Little is known about how proteostasis is maintained during viral infection. Here, the authors identify unexpected crosstalk between the calnexin cycle, ERAD, and reticulophagy, resulting in suppression of ebolavirus glycoprotein expression.
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Rozov SM, Deineko EV. Increasing the Efficiency of the Accumulation of Recombinant Proteins in Plant Cells: The Role of Transport Signal Peptides. PLANTS (BASEL, SWITZERLAND) 2022; 11:2561. [PMID: 36235427 PMCID: PMC9572730 DOI: 10.3390/plants11192561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The problem with increasing the yield of recombinant proteins is resolvable using different approaches, including the transport of a target protein to cell compartments with a low protease activity. In the cell, protein targeting involves short-signal peptide sequences recognized by intracellular protein transport systems. The main systems of the protein transport across membranes of the endoplasmic reticulum and endosymbiotic organelles are reviewed here, as are the major types and structure of the signal sequences targeting proteins to the endoplasmic reticulum and its derivatives, to plastids, and to mitochondria. The role of protein targeting to certain cell organelles depending on specific features of recombinant proteins and the effect of this targeting on the protein yield are discussed, in addition to the main directions of the search for signal sequences based on their primary structure. This knowledge makes it possible not only to predict a protein localization in the cell but also to reveal the most efficient sequences with potential biotechnological utility.
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Hirata T, Yang J, Tomida S, Tokoro Y, Kinoshita T, Fujita M, Kizuka Y. ER entry pathway and glycosylation of GPI-anchored proteins are determined by N-terminal signal sequence and C-terminal GPI-attachment sequence. J Biol Chem 2022; 298:102444. [PMID: 36055406 PMCID: PMC9520029 DOI: 10.1016/j.jbc.2022.102444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Newly synthesized proteins in the secretory pathway, including glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs), need to be correctly targeted and imported into the endoplasmic reticulum (ER) lumen. GPI-APs are synthesized in the cytosol as preproproteins, which contain an N-terminal signal sequence (SS), mature protein part, and C-terminal GPI-attachment sequence (GPI-AS), and translocated into the ER lumen where SS and GPI-AS are removed, generating mature GPI-APs. However, how various GPI-APs are translocated into the ER lumen in mammalian cells is unclear. Here, we investigated the ER entry pathways of GPI-APs using a panel of KO cells defective in each signal recognition particle–independent ER entry pathway—namely, Sec62, GET, or SND pathway. We found GPI-AP CD59 largely depends on the SND pathway for ER entry, whereas prion protein (Prion) and LY6K depend on both Sec62 and GET pathways. Using chimeric Prion and LY6K constructs in which the N-terminal SS or C-terminal GPI-AS was replaced with that of CD59, we revealed that the hydrophobicity of the SSs and GPI-ASs contributes to the dependence on Sec62 and GET pathways, respectively. Moreover, the ER entry route of chimeric Prion constructs with the C-terminal GPI-ASs replaced with that of CD59 was changed to the SND pathway. Simultaneously, their GPI structures and which oligosaccharyltransferase isoforms modify the constructs were altered without any amino acid change in the mature protein part. Taking these findings together, this study revealed N- and C-terminal sequences of GPI-APs determine the selective ER entry route, which in turn regulates subsequent maturation processes of GPI-APs.
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Affiliation(s)
- Tetsuya Hirata
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Jing Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Seita Tomida
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Yuko Tokoro
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Morihisa Fujita
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
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Arceo XG, Koslover EF, Zid BM, Brown AI. Mitochondrial mRNA localization is governed by translation kinetics and spatial transport. PLoS Comput Biol 2022; 18:e1010413. [PMID: 35984860 PMCID: PMC9432724 DOI: 10.1371/journal.pcbi.1010413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/31/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
For many nuclear-encoded mitochondrial genes, mRNA localizes to the mitochondrial surface co-translationally, aided by the association of a mitochondrial targeting sequence (MTS) on the nascent peptide with the mitochondrial import complex. For a subset of these co-translationally localized mRNAs, their localization is dependent on the metabolic state of the cell, while others are constitutively localized. To explore the differences between these two mRNA types we developed a stochastic, quantitative model for MTS-mediated mRNA localization to mitochondria in yeast cells. This model includes translation, applying gene-specific kinetics derived from experimental data; and diffusion in the cytosol. Even though both mRNA types are co-translationally localized we found that the steady state number, or density, of ribosomes along an mRNA was insufficient to differentiate the two mRNA types. Instead, conditionally-localized mRNAs have faster translation kinetics which modulate localization in combination with changes to diffusive search kinetics across metabolic states. Our model also suggests that the MTS requires a maturation time to become competent to bind mitochondria. Our work indicates that yeast cells can regulate mRNA localization to mitochondria by controlling mitochondrial volume fraction (influencing diffusive search times) and gene translation kinetics (adjusting mRNA binding competence) without the need for mRNA-specific binding proteins. These results shed light on both global and gene-specific mechanisms that enable cells to alter mRNA localization in response to changing metabolic conditions.
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Affiliation(s)
- Ximena G. Arceo
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Elena F. Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, United States of America
| | - Brian M. Zid
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Aidan I. Brown
- Department of Physics, Ryerson University, Toronto, Canada
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Synthesis, Biological Evaluation and Docking Studies of Ring-Opened Analogues of Ipomoeassin F. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144419. [PMID: 35889292 PMCID: PMC9320607 DOI: 10.3390/molecules27144419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
The plant-derived macrocyclic resin glycoside ipomoeassin F (Ipom-F) binds to Sec61α and significantly disrupts multiple aspects of Sec61-mediated protein biogenesis at the endoplasmic reticulum, ultimately leading to cell death. However, extensive assessment of Ipom-F as a molecular tool and a therapeutic lead is hampered by its limited production scale, largely caused by intramolecular assembly of the macrocyclic ring. Here, using in vitro and/or in cellula biological assays to explore the first series of ring-opened analogues for the ipomoeassins, and indeed all resin glycosides, we provide clear evidence that macrocyclic integrity is not required for the cytotoxic inhibition of Sec61-dependent protein translocation by Ipom-F. Furthermore, our modeling suggests that open-chain analogues of Ipom-F can interact with multiple sites on the Sec61α subunit, most likely located at a previously identified binding site for mycolactone and/or the so-called lateral gate. Subsequent in silico-aided design led to the discovery of the stereochemically simplified analogue 3 as a potent, alternative lead compound that could be synthesized much more efficiently than Ipom-F and will accelerate future ipomoeassin research in chemical biology and drug discovery. Our work may also inspire further exploration of ring-opened analogues of other resin glycosides.
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31
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Farkas Á, Urlaub H, Bohnsack KE, Schwappach B. Regulated targeting of the monotopic hairpin membrane protein Erg1 requires the GET pathway. J Biophys Biochem Cytol 2022; 221:213228. [PMID: 35587358 PMCID: PMC9123286 DOI: 10.1083/jcb.202201036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 02/08/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway targets C-terminally anchored transmembrane proteins and protects cells from lipotoxicity. Here, we reveal perturbed ergosterol production in ∆get3 cells and demonstrate the sensitivity of GET pathway mutants to the sterol synthesis inhibiting drug terbinafine. Our data uncover a key enzyme of sterol synthesis, the hairpin membrane protein squalene monooxygenase (Erg1), as a non-canonical GET pathway client, thus rationalizing the lipotoxicity phenotypes of GET pathway mutants. Get3 recognizes the hairpin targeting element of Erg1 via its classical client-binding pocket. Intriguingly, we find that the GET pathway is especially important for the acute upregulation of Erg1 induced by low sterol conditions. We further identify several other proteins anchored to the endoplasmic reticulum (ER) membrane exclusively via a hairpin as putative clients of the GET pathway. Our findings emphasize the necessity of dedicated targeting pathways for high-efficiency targeting of particular clients during dynamic cellular adaptation and highlight hairpin proteins as a potential novel class of GET clients.
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Affiliation(s)
- Ákos Farkas
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytic Mass Spectrometry, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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32
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Song J, Becker T. Fidelity of organellar protein targeting. Curr Opin Cell Biol 2022; 75:102071. [DOI: 10.1016/j.ceb.2022.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/26/2022]
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33
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Sicking M, Živná M, Bhadra P, Barešová V, Tirincsi A, Hadzibeganovic D, Hodaňová K, Vyleťal P, Sovová J, Jedličková I, Jung M, Bell T, Helms V, Bleyer AJ, Kmoch S, Cavalié A, Lang S. Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin. Life Sci Alliance 2022; 5:e202101150. [PMID: 35064074 PMCID: PMC8807872 DOI: 10.26508/lsa.202101150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
The human Sec61 complex is a widely distributed and abundant molecular machine. It resides in the membrane of the endoplasmic reticulum to channel two types of cargo: protein substrates and calcium ions. The SEC61A1 gene encodes for the pore-forming Sec61α subunit of the Sec61 complex. Despite their ubiquitous expression, the idiopathic SEC61A1 missense mutations p.V67G and p.T185A trigger a localized disease pattern diagnosed as autosomal dominant tubulointerstitial kidney disease (ADTKD-SEC61A1). Using cellular disease models for ADTKD-SEC61A1, we identified an impaired protein transport of the renal secretory protein renin and a reduced abundance of regulatory calcium transporters, including SERCA2. Treatment with the molecular chaperone phenylbutyrate reversed the defective protein transport of renin and the imbalanced calcium homeostasis. Signal peptide substitution experiments pointed at targeting sequences as the cause for the substrate-specific impairment of protein transport in the presence of the V67G or T185A mutations. Similarly, dominant mutations in the signal peptide of renin also cause ADTKD and point to impaired transport of this renal hormone as important pathogenic feature for ADTKD-SEC61A1 patients as well.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pratiti Bhadra
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Thomas Bell
- Department of Chemistry, University of Nevada, Reno, NV, USA
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anthony J Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Pre-clinical Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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Dahan N, Bykov YS, Boydston EA, Fadel A, Gazi Z, Hochberg-Laufer H, Martenson J, Denic V, Shav-Tal Y, Weissman JS, Aviram N, Zalckvar E, Schuldiner M. Peroxisome function relies on organelle-associated mRNA translation. SCIENCE ADVANCES 2022; 8:eabk2141. [PMID: 35020435 PMCID: PMC8754406 DOI: 10.1126/sciadv.abk2141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/18/2021] [Indexed: 05/26/2023]
Abstract
Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.
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Affiliation(s)
- Noa Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yury S. Bykov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elizabeth A. Boydston
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Gazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - James Martenson
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Vlad Denic
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, The Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Naama Aviram
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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Reduced DNAJC3 Expression Affects Protein Translocation across the ER Membrane and Attenuates the Down-Modulating Effect of the Translocation Inhibitor Cyclotriazadisulfonamide. Int J Mol Sci 2022; 23:ijms23020584. [PMID: 35054769 PMCID: PMC8775681 DOI: 10.3390/ijms23020584] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
One of the reported substrates for the endoplasmic reticulum (ER) translocation inhibitor cyclotriazadisulfonamide (CADA) is DNAJC3, a chaperone of the unfolded protein response during ER stress. In this study, we investigated the impact of altered DNAJC3 protein levels on the inhibitory activity of CADA. By comparing WT DNAJC3 with a CADA-resistant DNAJC3 mutant, we observed the enhanced sensitivity of human CD4, PTK7 and ERLEC1 for CADA when DNAJC3 was expressed at high levels. Combined treatment of CADA with a proteasome inhibitor resulted in synergistic inhibition of protein translocation and in the rescue of a small preprotein fraction, which presumably corresponds to the CADA affected protein fraction that is stalled at the Sec61 translocon. We demonstrate that DNAJC3 enhances the protein translation of a reporter protein that is expressed downstream of the CADA-stalled substrate, suggesting that DNAJC3 promotes the clearance of the clogged translocon. We propose a model in which a reduced DNAJC3 level by CADA slows down the clearance of CADA-stalled substrates. This results in higher residual translocation into the ER lumen due to the longer dwelling time of the temporarily stalled substrates in the translocon. Thus, by directly reducing DNAJC3 protein levels, CADA attenuates its net down-modulating effect on its substrates.
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36
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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Park J, Chang J, Hwang HJ, Jeong K, Lee HJ, Ha H, Park Y, Lim C, Woo JS, Kim YK. The pioneer round of translation ensures proper targeting of ER and mitochondrial proteins. Nucleic Acids Res 2021; 49:12517-12534. [PMID: 34850140 PMCID: PMC8643669 DOI: 10.1093/nar/gkab1098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The pioneer (or first) round of translation of newly synthesized mRNAs is largely mediated by a nuclear cap-binding complex (CBC). In a transcriptome-wide analysis of polysome-associated and CBC-bound transcripts, we identify RN7SL1, a noncoding RNA component of a signal recognition particle (SRP), as an interaction partner of the CBC. The direct CBC–SRP interaction safeguards against abnormal expression of polypeptides from a ribosome–nascent chain complex (RNC)–SRP complex until the latter is properly delivered to the endoplasmic reticulum. Failure of this surveillance causes abnormal expression of misfolded proteins at inappropriate intracellular locations, leading to a cytosolic stress response. This surveillance pathway also blocks protein synthesis through RNC–SRP misassembled on an mRNA encoding a mitochondrial protein. Thus, our results reveal a surveillance pathway in which pioneer translation ensures proper targeting of endoplasmic reticulum and mitochondrial proteins.
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Affiliation(s)
- Joori Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jeeyoon Chang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyun Jung Hwang
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Kwon Jeong
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hyuk-Joon Lee
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Hongseok Ha
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yeonkyoung Park
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Chunghun Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae-Sung Woo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, Republic of Korea.,Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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38
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Zimmermann R, Lang S, Lerner M, Förster F, Nguyen D, Helms V, Schrul B. Quantitative Proteomics and Differential Protein Abundance Analysis after the Depletion of PEX3 from Human Cells Identifies Additional Aspects of Protein Targeting to the ER. Int J Mol Sci 2021; 22:ijms222313028. [PMID: 34884833 PMCID: PMC8658024 DOI: 10.3390/ijms222313028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/19/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Protein import into the endoplasmic reticulum (ER) is the first step in the biogenesis of around 10,000 different soluble and membrane proteins in humans. It involves the co- or post-translational targeting of precursor polypeptides to the ER, and their subsequent membrane insertion or translocation. So far, three pathways for the ER targeting of precursor polypeptides and four pathways for the ER targeting of mRNAs have been described. Typically, these pathways deliver their substrates to the Sec61 polypeptide-conducting channel in the ER membrane. Next, the precursor polypeptides are inserted into the ER membrane or translocated into the ER lumen, which may involve auxiliary translocation components, such as the TRAP and Sec62/Sec63 complexes, or auxiliary membrane protein insertases, such as EMC and the TMCO1 complex. Recently, the PEX19/PEX3-dependent pathway, which has a well-known function in targeting and inserting various peroxisomal membrane proteins into pre-existent peroxisomal membranes, was also found to act in the targeting and, putatively, insertion of monotopic hairpin proteins into the ER. These either remain in the ER as resident ER membrane proteins, or are pinched off from the ER as components of new lipid droplets. Therefore, the question arose as to whether this pathway may play a more general role in ER protein targeting, i.e., whether it represents a fourth pathway for the ER targeting of precursor polypeptides. Thus, we addressed the client spectrum of the PEX19/PEX3-dependent pathway in both PEX3-depleted HeLa cells and PEX3-deficient Zellweger patient fibroblasts by an established approach which involved the label-free quantitative mass spectrometry of the total proteome of depleted or deficient cells, as well as differential protein abundance analysis. The negatively affected proteins included twelve peroxisomal proteins and two hairpin proteins of the ER, thus confirming two previously identified classes of putative PEX19/PEX3 clients in human cells. Interestingly, fourteen collagen-related proteins with signal peptides or N-terminal transmembrane helices belonging to the secretory pathway were also negatively affected by PEX3 deficiency, which may suggest compromised collagen biogenesis as a hitherto-unknown contributor to organ failures in the respective Zellweger patients.
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Affiliation(s)
- Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (D.N.); (V.H.)
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.L.); (M.L.)
- Correspondence: (R.Z.); (B.S.)
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39
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Take Me Home, Protein Roads: Structural Insights into Signal Peptide Interactions during ER Translocation. Int J Mol Sci 2021; 22:ijms222111871. [PMID: 34769302 PMCID: PMC8584900 DOI: 10.3390/ijms222111871] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/14/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Cleavable endoplasmic reticulum (ER) signal peptides (SPs) and other non-cleavable signal sequences target roughly a quarter of the human proteome to the ER. These short peptides, mostly located at the N-termini of proteins, are highly diverse. For most proteins targeted to the ER, it is the interactions between the signal sequences and the various ER targeting and translocation machineries such as the signal recognition particle (SRP), the protein-conducting channel Sec61, and the signal peptidase complex (SPC) that determine the proteins’ target location and provide translocation fidelity. In this review, we follow the signal peptide into the ER and discuss the recent insights that structural biology has provided on the governing principles of those interactions.
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40
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Link F, Borges AR, Jones NG, Engstler M. To the Surface and Back: Exo- and Endocytic Pathways in Trypanosoma brucei. Front Cell Dev Biol 2021; 9:720521. [PMID: 34422837 PMCID: PMC8377397 DOI: 10.3389/fcell.2021.720521] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/06/2021] [Indexed: 01/10/2023] Open
Abstract
Trypanosoma brucei is one of only a few unicellular pathogens that thrives extracellularly in the vertebrate host. Consequently, the cell surface plays a critical role in both immune recognition and immune evasion. The variant surface glycoprotein (VSG) coats the entire surface of the parasite and acts as a flexible shield to protect invariant proteins against immune recognition. Antigenic variation of the VSG coat is the major virulence mechanism of trypanosomes. In addition, incessant motility of the parasite contributes to its immune evasion, as the resulting fluid flow on the cell surface drags immunocomplexes toward the flagellar pocket, where they are internalized. The flagellar pocket is the sole site of endo- and exocytosis in this organism. After internalization, VSG is rapidly recycled back to the surface, whereas host antibodies are thought to be transported to the lysosome for degradation. For this essential step to work, effective machineries for both sorting and recycling of VSGs must have evolved in trypanosomes. Our understanding of the mechanisms behind VSG recycling and VSG secretion, is by far not complete. This review provides an overview of the trypanosome secretory and endosomal pathways. Longstanding questions are pinpointed that, with the advent of novel technologies, might be answered in the near future.
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Affiliation(s)
- Fabian Link
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alyssa R Borges
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Nicola G Jones
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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41
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Impact of Membrane Lipids on UapA and AzgA Transporter Subcellular Localization and Activity in Aspergillus nidulans. J Fungi (Basel) 2021; 7:jof7070514. [PMID: 34203131 PMCID: PMC8304608 DOI: 10.3390/jof7070514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/21/2022] Open
Abstract
Recent biochemical and biophysical evidence have established that membrane lipids, namely phospholipids, sphingolipids and sterols, are critical for the function of eukaryotic plasma membrane transporters. Here, we study the effect of selected membrane lipid biosynthesis mutations and of the ergosterol-related antifungal itraconazole on the subcellular localization, stability and transport kinetics of two well-studied purine transporters, UapA and AzgA, in Aspergillus nidulans. We show that genetic reduction in biosynthesis of ergosterol, sphingolipids or phosphoinositides arrest A. nidulans growth after germling formation, but solely blocks in early steps of ergosterol (Erg11) or sphingolipid (BasA) synthesis have a negative effect on plasma membrane (PM) localization and stability of transporters before growth arrest. Surprisingly, the fraction of UapA or AzgA that reaches the PM in lipid biosynthesis mutants is shown to conserve normal apparent transport kinetics. We further show that turnover of UapA, which is the transporter mostly sensitive to membrane lipid content modification, occurs during its trafficking and by enhanced endocytosis, and is partly dependent on autophagy and Hect-type HulARsp5 ubiquitination. Our results point out that the role of specific membrane lipids on transporter biogenesis and function in vivo is complex, combinatorial and transporter-dependent.
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42
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Dederer V, Lemberg MK. Transmembrane dislocases: a second chance for protein targeting. Trends Cell Biol 2021; 31:898-911. [PMID: 34147299 DOI: 10.1016/j.tcb.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/31/2022]
Abstract
Precise distribution of proteins is essential to sustain the viability of cells. A complex network of protein synthesis and targeting factors cooperate with protein quality control systems to ensure protein homeostasis. Defective proteins are inevitably degraded by the ubiquitin-proteasome system and lysosomes. However, due to overlapping targeting information and limited targeting fidelity, certain proteins become mislocalized. In this review, we present the idea that transmembrane dislocases recognize and remove mislocalized membrane proteins from cellular organelles. This enables other targeting attempts and prevents degradation of mislocalized but otherwise functional proteins. These transmembrane dislocases can be found in the outer mitochondrial membrane (OMM) and endoplasmic reticulum (ER). We highlight common principles regarding client recognition and outline open questions in our understanding of transmembrane dislocases.
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Affiliation(s)
- Verena Dederer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Current address: Institute for Pharmaceutical Biology and Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany.
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43
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Bhadra P, Schorr S, Lerner M, Nguyen D, Dudek J, Förster F, Helms V, Lang S, Zimmermann R. Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER. Molecules 2021; 26:3591. [PMID: 34208277 PMCID: PMC8230838 DOI: 10.3390/molecules26123591] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.
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Affiliation(s)
- Pratiti Bhadra
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Duy Nguyen
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Volkhard Helms
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66041 Saarbrücken, Germany; (P.B.); (D.N.); (V.H.)
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (S.S.); (M.L.); (J.D.); (S.L.)
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44
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Fenech EJ, Ben-Dor S, Schuldiner M. Double the Fun, Double the Trouble: Paralogs and Homologs Functioning in the Endoplasmic Reticulum. Annu Rev Biochem 2021; 89:637-666. [PMID: 32569522 DOI: 10.1146/annurev-biochem-011520-104831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of eukaryotic genomes has been propelled by a series of gene duplication events, leading to an expansion in new functions and pathways. While duplicate genes may retain some functional redundancy, it is clear that to survive selection they cannot simply serve as a backup but rather must acquire distinct functions required for cellular processes to work accurately and efficiently. Understanding these differences and characterizing gene-specific functions is complex. Here we explore different gene pairs and families within the context of the endoplasmic reticulum (ER), the main cellular hub of lipid biosynthesis and the entry site for the secretory pathway. Focusing on each of the ER functions, we highlight specificities of related proteins and the capabilities conferred to cells through their conservation. More generally, these examples suggest why related genes have been maintained by evolutionary forces and provide a conceptual framework to experimentally determine why they have survived selection.
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Affiliation(s)
- Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
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45
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Lashkevich KA, Dmitriev SE. mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts. Mol Biol 2021; 55:507-537. [PMID: 34092811 PMCID: PMC8164833 DOI: 10.1134/s0026893321030080] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 02/26/2021] [Accepted: 03/12/2021] [Indexed: 12/28/2022]
Abstract
Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
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Affiliation(s)
- Kseniya A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119234 Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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46
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Lee JH, Jomaa A, Chung S, Hwang Fu YH, Qian R, Sun X, Hsieh HH, Chandrasekar S, Bi X, Mattei S, Boehringer D, Weiss S, Ban N, Shan SO. Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER. SCIENCE ADVANCES 2021; 7:eabg0942. [PMID: 34020957 PMCID: PMC8139590 DOI: 10.1126/sciadv.abg0942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/01/2021] [Indexed: 05/07/2023]
Abstract
The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.
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Affiliation(s)
- Jae Ho Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ahmad Jomaa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu-Hsien Hwang Fu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ruilin Qian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xuemeng Sun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hao-Hsuan Hsieh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Simone Mattei
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
- Cryo-EM Knowledge Hub, ETH Zurich, 8093 Zurich, Switzerland
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, 52900 Ramat-Gan, Israel
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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47
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Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
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Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
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48
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Sicking M, Lang S, Bochen F, Roos A, Drenth JPH, Zakaria M, Zimmermann R, Linxweiler M. Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex. Cells 2021; 10:1036. [PMID: 33925740 PMCID: PMC8147068 DOI: 10.3390/cells10051036] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/14/2022] Open
Abstract
The rough endoplasmic reticulum (ER) of nucleated human cells has crucial functions in protein biogenesis, calcium (Ca2+) homeostasis, and signal transduction. Among the roughly one hundred components, which are involved in protein import and protein folding or assembly, two components stand out: The Sec61 complex and BiP. The Sec61 complex in the ER membrane represents the major entry point for precursor polypeptides into the membrane or lumen of the ER and provides a conduit for Ca2+ ions from the ER lumen to the cytosol. The second component, the Hsp70-type molecular chaperone immunoglobulin heavy chain binding protein, short BiP, plays central roles in protein folding and assembly (hence its name), protein import, cellular Ca2+ homeostasis, and various intracellular signal transduction pathways. For the purpose of this review, we focus on these two components, their relevant allosteric effectors and on the question of how their respective functional cycles are linked in order to reconcile the apparently contradictory features of the ER membrane, selective permeability for precursor polypeptides, and impermeability for Ca2+. The key issues are that the Sec61 complex exists in two conformations: An open and a closed state that are in a dynamic equilibrium with each other, and that BiP contributes to its gating in both directions in cooperation with different co-chaperones. While the open Sec61 complex forms an aqueous polypeptide-conducting- and transiently Ca2+-permeable channel, the closed complex is impermeable even to Ca2+. Therefore, we discuss the human hereditary and tumor diseases that are linked to Sec61 channel gating, termed Sec61-channelopathies, as disturbances of selective polypeptide-impermeability and/or aberrant Ca2+-permeability.
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Affiliation(s)
- Mark Sicking
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Sven Lang
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Florian Bochen
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
| | - Andreas Roos
- Department of Neuropediatrics, Essen University Hospital, D-45147 Essen, Germany;
| | - Joost P. H. Drenth
- Department of Molecular Gastroenterology and Hepatology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Muhammad Zakaria
- Department of Genetics, Hazara University, Mansehra 21300, Pakistan;
| | - Richard Zimmermann
- Department of Medical Biochemistry & Molecular Biology, Saarland University, D-66421 Homburg, Germany;
| | - Maximilian Linxweiler
- Department of Otorhinolaryngology, Head and Neck Surgery, Saarland University Medical Center, D-66421 Homburg, Germany; (F.B.); (M.L.)
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49
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Lautier O, Penzo A, Rouvière JO, Chevreux G, Collet L, Loïodice I, Taddei A, Devaux F, Collart MA, Palancade B. Co-translational assembly and localized translation of nucleoporins in nuclear pore complex biogenesis. Mol Cell 2021; 81:2417-2427.e5. [PMID: 33838103 DOI: 10.1016/j.molcel.2021.03.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/24/2021] [Accepted: 03/18/2021] [Indexed: 01/03/2023]
Abstract
mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N-termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus.
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Affiliation(s)
- Ophélie Lautier
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Arianna Penzo
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Jérôme O Rouvière
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Guillaume Chevreux
- ProteoSeine@IJM, Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Louis Collet
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Isabelle Loïodice
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, UMR3664 Nuclear Dynamics, Paris, France
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de biologie Paris-Seine (IBPS), UMR 7238, Laboratoire de biologie computationnelle et quantitative, LCQB, 4 place Jussieu, 75005 Paris, France
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France.
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50
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Zhang Y, De Laurentiis E, Bohnsack KE, Wahlig M, Ranjan N, Gruseck S, Hackert P, Wölfle T, Rodnina MV, Schwappach B, Rospert S. Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast. Nat Commun 2021; 12:782. [PMID: 33542241 PMCID: PMC7862611 DOI: 10.1038/s41467-021-20981-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway assists in the posttranslational delivery of tail-anchored proteins, containing a single C-terminal transmembrane domain, to the ER. Here we uncover how the yeast GET pathway component Get4/5 facilitates capture of tail-anchored proteins by Sgt2, which interacts with tail-anchors and hands them over to the targeting component Get3. Get4/5 binds directly and with high affinity to ribosomes, positions Sgt2 close to the ribosomal tunnel exit, and facilitates the capture of tail-anchored proteins by Sgt2. The contact sites of Get4/5 on the ribosome overlap with those of SRP, the factor mediating cotranslational ER-targeting. Exposure of internal transmembrane domains at the tunnel exit induces high-affinity ribosome binding of SRP, which in turn prevents ribosome binding of Get4/5. In this way, the position of a transmembrane domain within nascent ER-targeted proteins mediates partitioning into either the GET or SRP pathway directly at the ribosomal tunnel exit. The guided entry of tail-anchored proteins (GET) pathway assists in the delivery of such proteins to the ER. Here, the authors reveal that the pathway components Get4/5 probe a region near the ribosomal exit tunnel. Upon emergence of a client protein, Get4/5 recruits Sgt2 and initiates the targeting phase of the pathway.
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Affiliation(s)
- Ying Zhang
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Evelina De Laurentiis
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Mascha Wahlig
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Namit Ranjan
- Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Simon Gruseck
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Marina V Rodnina
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.,Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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